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Abstract: We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed.
Title: A note on the separability index
Abstract: In discriminating between objects from different classes, the more separable these classes are the less computationally expensive and complex a classifier can be used. One thus seeks a measure that can quickly capture this separability concept between classes whilst having an intuitive interpretation on what it is quantifying. A previously proposed separability measure, the separability index (SI) has been shown to intuitively capture the class separability property very well. This short note highlights the limitations of this measure and proposes a slight variation to it by combining it with another form of separability measure that captures a quantity not covered by the Separability Index.
Title: An analysis of a random algorithm for estimating all the matchings
Abstract: Counting the number of all the matchings on a bipartite graph has been transformed into calculating the permanent of a matrix obtained from the extended bipartite graph by Yan Huo, and Rasmussen presents a simple approach (RM) to approximate the permanent, which just yields a critical ratio O($n\omega(n)$) for almost all the 0-1 matrices, provided it's a simple promising practical way to compute this #P-complete problem. In this paper, the performance of this method will be shown when it's applied to compute all the matchings based on that transformation. The critical ratio will be proved to be very large with a certain probability, owning an increasing factor larger than any polynomial of $n$ even in the sense for almost all the 0-1 matrices. Hence, RM fails to work well when counting all the matchings via computing the permanent of the matrix. In other words, we must carefully utilize the known methods of estimating the permanent to count all the matchings through that transformation.
Title: Emerge-Sort: Converging to Ordered Sequences by Simple Local Operators
Abstract: In this paper we examine sorting on the assumption that we do not know in advance which way to sort a sequence of numbers and we set at work simple local comparison and swap operators whose repeating application ends up in sorted sequences. These are the basic elements of Emerge-Sort, our approach to self-organizing sorting, which we then validate experimentally across a range of samples. Observing an O(n2) run-time behaviour, we note that the n/logn delay coefficient that differentiates Emerge-Sort from the classical comparison based algorithms is an instantiation of the price of anarchy we pay for not imposing a sorting order and for letting that order emerge through the local interactions.
Title: A novel changepoint detection algorithm
Abstract: We propose an algorithm for simultaneously detecting and locating changepoints in a time series, and a framework for predicting the distribution of the next point in the series. The kernel of the algorithm is a system of equations that computes, for each index i, the probability that the last (most recent) change point occurred at i. We evaluate this algorithm by applying it to the change point detection problem and comparing it to the generalized likelihood ratio (GLR) algorithm. We find that our algorithm is as good as GLR, or better, over a wide range of scenarios, and that the advantage increases as the signal-to-noise ratio decreases.
Title: Decomposition Principles and Online Learning in Cross-Layer Optimization for Delay-Sensitive Applications
Abstract: In this paper, we propose a general cross-layer optimization framework in which we explicitly consider both the heterogeneous and dynamically changing characteristics of delay-sensitive applications and the underlying time-varying network conditions. We consider both the independently decodable data units (DUs, e.g. packets) and the interdependent DUs whose dependencies are captured by a directed acyclic graph (DAG). We first formulate the cross-layer design as a non-linear constrained optimization problem by assuming complete knowledge of the application characteristics and the underlying network conditions. The constrained cross-layer optimization is decomposed into several cross-layer optimization subproblems for each DU and two master problems. The proposed decomposition method determines the necessary message exchanges between layers for achieving the optimal cross-layer solution. However, the attributes (e.g. distortion impact, delay deadline etc) of future DUs as well as the network conditions are often unknown in the considered real-time applications. The impact of current cross-layer actions on the future DUs can be characterized by a state-value function in the Markov decision process (MDP) framework. Based on the dynamic programming solution to the MDP, we develop a low-complexity cross-layer optimization algorithm using online learning for each DU transmission. This online algorithm can be implemented in real-time in order to cope with unknown source characteristics, network dynamics and resource constraints. Our numerical results demonstrate the efficiency of the proposed online algorithm.
Title: Obtaining Depth Maps From Color Images By Region Based Stereo Matching Algorithms
Abstract: In the paper, region based stereo matching algorithms are developed for extraction depth information from two color stereo image pair. A filter eliminating unreliable disparity estimation was used for increasing reliability of the disparity map. Obtained results by algorithms were represented and compared.
Title: A Novel Clustering Algorithm Based on Quantum Random Walk
Abstract: The enormous successes have been made by quantum algorithms during the last decade. In this paper, we combine the quantum random walk (QRW) with the problem of data clustering, and develop two clustering algorithms based on the one dimensional QRW. Then, the probability distributions on the positions induced by QRW in these algorithms are investigated, which also indicates the possibility of obtaining better results. Consequently, the experimental results have demonstrated that data points in datasets are clustered reasonably and efficiently, and the clustering algorithms are of fast rates of convergence. Moreover, the comparison with other algorithms also provides an indication of the effectiveness of the proposed approach.
Title: Optimal sequential testing of two simple hypotheses in presence of control variables
Abstract: Suppose that at any stage of a statistical experiment a control variable $X$ that affects the distribution of the observed data $Y$ can be used. The distribution of $Y$ depends on some unknown parameter $\theta$, and we consider the classical problem of testing a simple hypothesis $H_0: \theta=\theta_0$ against a simple alternative $H_1: \theta=\theta_1$ allowing the data to be controlled by $X$, in the following sequential context. The experiment starts with assigning a value $X_1$ to the control variable and observing $Y_1$ as a response. After some analysis, we choose another value $X_2$ for the control variable, and observe $Y_2$ as a response, etc. It is supposed that the experiment eventually stops, and at that moment a final decision in favour of $H_0$ or $H_1$ is to be taken. In this article, our aim is to characterize the structure of optimal sequential procedures, based on this type of data, for testing a simple hypothesis against a simple alternative.
Title: Logic programs with propositional connectives and aggregates
Abstract: Answer set programming (ASP) is a logic programming paradigm that can be used to solve complex combinatorial search problems. Aggregates are an ASP construct that plays an important role in many applications. Defining a satisfactory semantics of aggregates turned out to be a difficult problem, and in this paper we propose a new approach, based on an analogy between aggregates and propositional connectives. First, we extend the definition of an answer set/stable model to cover arbitrary propositional theories; then we define aggregates on top of them both as primitive constructs and as abbreviations for formulas. Our definition of an aggregate combines expressiveness and simplicity, and it inherits many theorems about programs with nested expressions, such as theorems about strong equivalence and splitting.
Title: Parallel hierarchical sampling: a practical multiple-chains sampler for Bayesian model selection
Abstract: This paper introduces the parallel hierarchical sampler (PHS), a Markov chain Monte Carlo algorithm using several chains simultaneously. The connections between PHS and the parallel tempering (PT) algorithm are illustrated, convergence of PHS joint transition kernel is proved and and its practical advantages are emphasized. We illustrate the inferences obtained using PHS, parallel tempering and the Metropolis-Hastings algorithm for three Bayesian model selection problems, namely Gaussian clustering, the selection of covariates for a linear regression model and the selection of the structure of a treed survival model.
Title: Comparison of Data Imputation Techniques and their Impact
Abstract: Missing and incomplete information in surveys or databases can be imputed using different statistical and soft-computing techniques. This paper comprehensively compares auto-associative neural networks (NN), neuro-fuzzy (NF) systems and the hybrid combinations the above methods with hot-deck imputation. The tests are conducted on an eight category antenatal survey and also under principal component analysis (PCA) conditions. The neural network outperforms the neuro-fuzzy system for all tests by an average of 5.8%, while the hybrid method is on average 15.9% more accurate yet 50% less computationally efficient than the NN or NF systems acting alone. The global impact assessment of the imputed data is performed by several statistical tests. It is found that although the imputed accuracy is high, the global effect of the imputed data causes the PCA inter-relationships between the dataset to become altered. The standard deviation of the imputed dataset is on average 36.7% lower than the actual dataset which may cause an incorrect interpretation of the results.
Title: Multi-Agent Reinforcement Learning and Genetic Policy Sharing
Abstract: The effects of policy sharing between agents in a multi-agent dynamical system has not been studied extensively. I simulate a system of agents optimizing the same task using reinforcement learning, to study the effects of different population densities and policy sharing. I demonstrate that sharing policies decreases the time to reach asymptotic behavior, and results in improved asymptotic behavior.
Title: Missing Data using Decision Forest and Computational Intelligence
Abstract: Autoencoder neural network is implemented to estimate the missing data. Genetic algorithm is implemented for network optimization and estimating the missing data. Missing data is treated as Missing At Random mechanism by implementing maximum likelihood algorithm. The network performance is determined by calculating the mean square error of the network prediction. The network is further optimized by implementing Decision Forest. The impact of missing data is then investigated and decision forrests are found to improve the results.
Title: Simultaneous confidence intervals for the population cell means, for two-by-two factorial data, that utilize uncertain prior information
Abstract: Consider a two-by-two factorial experiment with more than 1 replicate. Suppose that we have uncertain prior information that the two-factor interaction is zero. We describe new simultaneous frequentist confidence intervals for the 4 population cell means, with simultaneous confidence coefficient 1-alpha, that utilize this prior information in the following sense. These simultaneous confidence intervals define a cube with expected volume that (a) is relatively small when the two-factor interaction is zero and (b) has maximum value that is not too large. Also, these intervals coincide with the standard simultaneous confidence intervals obtained by Tukey's method, with simultaneous confidence coefficient 1-alpha, when the data strongly contradict the prior information that the two-factor interaction is zero. We illustrate the application of these new simultaneous confidence intervals to a real data set.
Title: Estimating limits from Poisson counting data using Dempster--Shafer analysis
Abstract: We present a Dempster--Shafer (DS) approach to estimating limits from Poisson counting data with nuisance parameters. Dempster--Shafer is a statistical framework that generalizes Bayesian statistics. DS calculus augments traditional probability by allowing mass to be distributed over power sets of the event space. This eliminates the Bayesian dependence on prior distributions while allowing the incorporation of prior information when it is available. We use the Poisson Dempster--Shafer model (DSM) to derive a posterior DSM for the ``Banff upper limits challenge'' three-Poisson model. The results compare favorably with other approaches, demonstrating the utility of the approach. We argue that the reduced dependence on priors afforded by the Dempster--Shafer framework is both practically and theoretically desirable.
Title: Identification of parameters underlying emotions and a classification of emotions
Abstract: The standard classification of emotions involves categorizing the expression of emotions. In this paper, parameters underlying some emotions are identified and a new classification based on these parameters is suggested.
Title: Convex Sparse Matrix Factorizations
Abstract: We present a convex formulation of dictionary learning for sparse signal decomposition. Convexity is obtained by replacing the usual explicit upper bound on the dictionary size by a convex rank-reducing term similar to the trace norm. In particular, our formulation introduces an explicit trade-off between size and sparsity of the decomposition of rectangular matrices. Using a large set of synthetic examples, we compare the estimation abilities of the convex and non-convex approaches, showing that while the convex formulation has a single local minimum, this may lead in some cases to performance which is inferior to the local minima of the non-convex formulation.
Title: Trek separation for Gaussian graphical models
Abstract: Gaussian graphical models are semi-algebraic subsets of the cone of positive definite covariance matrices. Submatrices with low rank correspond to generalizations of conditional independence constraints on collections of random variables. We give a precise graph-theoretic characterization of when submatrices of the covariance matrix have small rank for a general class of mixed graphs that includes directed acyclic and undirected graphs as special cases. Our new trek separation criterion generalizes the familiar $d$-separation criterion. Proofs are based on the trek rule, the resulting matrix factorizations and classical theorems of algebraic combinatorics on the expansions of determinants of path polynomials.
Title: Prediction with Restricted Resources and Finite Automata
Abstract: We obtain an index of the complexity of a random sequence by allowing the role of the measure in classical probability theory to be played by a function we call the generating mechanism. Typically, this generating mechanism will be a finite automata. We generate a set of biased sequences by applying a finite state automata with a specified number, $m$, of states to the set of all binary sequences. Thus we can index the complexity of our random sequence by the number of states of the automata. We detail optimal algorithms to predict sequences generated in this way.
Title: An Ensemble Kalman-Particle Predictor-Corrector Filter for Non-Gaussian Data Assimilation
Abstract: An Ensemble Kalman Filter (EnKF, the predictor) is used make a large change in the state, followed by a Particle Filer (PF, the corrector) which assigns importance weights to describe non-Gaussian distribution. The weights are obtained by nonparametric density estimation. It is demonstrated on several numerical examples that the new predictor-corrector filter combines the advantages of the EnKF and the PF and that it is suitable for high dimensional states which are discretizations of solutions of partial differential equations.
Title: Characterizing Truthful Multi-Armed Bandit Mechanisms
Abstract: We consider a multi-round auction setting motivated by pay-per-click auctions for Internet advertising. In each round the auctioneer selects an advertiser and shows her ad, which is then either clicked or not. An advertiser derives value from clicks; the value of a click is her private information. Initially, neither the auctioneer nor the advertisers have any information about the likelihood of clicks on the advertisements. The auctioneer's goal is to design a (dominant strategies) truthful mechanism that (approximately) maximizes the social welfare. If the advertisers bid their true private values, our problem is equivalent to the "multi-armed bandit problem", and thus can be viewed as a strategic version of the latter. In particular, for both problems the quality of an algorithm can be characterized by "regret", the difference in social welfare between the algorithm and the benchmark which always selects the same "best" advertisement. We investigate how the design of multi-armed bandit algorithms is affected by the restriction that the resulting mechanism must be truthful. We find that truthful mechanisms have certain strong structural properties -- essentially, they must separate exploration from exploitation -- and they incur much higher regret than the optimal multi-armed bandit algorithms. Moreover, we provide a truthful mechanism which (essentially) matches our lower bound on regret.
Title: Classification of Cell Images Using MPEG-7-influenced Descriptors and Support Vector Machines in Cell Morphology
Abstract: Counting and classifying blood cells is an important diagnostic tool in medicine. Support Vector Machines are increasingly popular and efficient and could replace artificial neural network systems. Here a method to classify blood cells is proposed using SVM. A set of statistics on images are implemented in C++. The MPEG-7 descriptors Scalable Color Descriptor, Color Structure Descriptor, Color Layout Descriptor and Homogeneous Texture Descriptor are extended in size and combined with textural features corresponding to textural properties perceived visually by humans. From a set of images of human blood cells these statistics are collected. A SVM is implemented and trained to classify the cell images. The cell images come from a CellaVision DM-96 machine which classify cells from images from microscopy. The output images and classification of the CellaVision machine is taken as ground truth, a truth that is 90-95% correct. The problem is divided in two -- the primary and the simplified. The primary problem is to classify the same classes as the CellaVision machine. The simplified problem is to differ between the five most common types of white blood cells. An encouraging result is achieved in both cases -- error rates of 10.8% and 3.1% -- considering that the SVM is misled by the errors in ground truth. Conclusion is that further investigation of performance is worthwhile.
Title: Urologic robots and future directions
Abstract: PURPOSE OF REVIEW: Robot-assisted laparoscopic surgery in urology has gained immense popularity with the daVinci system, but a lot of research teams are working on new robots. The purpose of this study is to review current urologic robots and present future development directions. RECENT FINDINGS: Future systems are expected to advance in two directions: improvements of remote manipulation robots and developments of image-guided robots. SUMMARY: The final goal of robots is to allow safer and more homogeneous outcomes with less variability of surgeon performance, as well as new tools to perform tasks on the basis of medical transcutaneous imaging, in a less invasive way, at lower costs. It is expected that improvements for a remote system could be augmented in reality, with haptic feedback, size reduction, and development of new tools for natural orifice translumenal endoscopic surgery. The paradigm of image-guided robots is close to clinical availability and the most advanced robots are presented with end-user technical assessments. It is also notable that the potential of robots lies much further ahead than the accomplishments of the daVinci system. The integration of imaging with robotics holds a substantial promise, because this can accomplish tasks otherwise impossible. Image-guided robots have the potential to offer a paradigm shift.
Title: Physics of risk and uncertainty in quantum decision making
Abstract: The Quantum Decision Theory, developed recently by the authors, is applied to clarify the role of risk and uncertainty in decision making and in particular in relation to the phenomenon of dynamic inconsistency. By formulating this notion in precise mathematical terms, we distinguish three types of inconsistency: time inconsistency, planning paradox, and inconsistency occurring in some discounting effects. While time inconsistency is well accounted for in classical decision theory, the planning paradox is in contradiction with classical utility theory. It finds a natural explanation in the frame of the Quantum Decision Theory. Different types of discounting effects are analyzed and shown to enjoy a straightforward explanation within the suggested theory. We also introduce a general methodology based on self-similar approximation theory for deriving the evolution equations for the probabilities of future prospects. This provides a novel classification of possible discount factors, which include the previously known cases (exponential or hyperbolic discounting), but also predicts a novel class of discount factors that decay to a strictly positive constant for very large future time horizons. This class may be useful to deal with very long-term discounting situations associated with intergenerational public policy choices, encompassing issues such as global warming and nuclear waste disposal.
Title: A New Trend in Optimization on Multi Overcomplete Dictionary toward Inpainting
Abstract: Recently, great attention was intended toward overcomplete dictionaries and the sparse representations they can provide. In a wide variety of signal processing problems, sparsity serves a crucial property leading to high performance. Inpainting, the process of reconstructing lost or deteriorated parts of images or videos, is an interesting application which can be handled by suitably decomposition of an image through combination of overcomplete dictionaries. This paper addresses a novel technique of such a decomposition and investigate that through inpainting of images. Simulations are presented to demonstrate the validation of our approach.
Title: Probabilistic SVM/GMM Classifier for Speaker-Independent Vowel Recognition in Continues Speech
Abstract: In this paper, we discuss the issues in automatic recognition of vowels in Persian language. The present work focuses on new statistical method of recognition of vowels as a basic unit of syllables. First we describe a vowel detection system then briefly discuss how the detected vowels can feed to recognition unit. According to pattern recognition, Support Vector Machines (SVM) as a discriminative classifier and Gaussian mixture model (GMM) as a generative model classifier are two most popular techniques. Current state-ofthe- art systems try to combine them together for achieving more power of classification and improving the performance of the recognition systems. The main idea of the study is to combine probabilistic SVM and traditional GMM pattern classification with some characteristic of speech like band-pass energy to achieve better classification rate. This idea has been analytically formulated and tested on a FarsDat based vowel recognition system. The results show inconceivable increases in recognition accuracy. The tests have been carried out by various proposed vowel recognition algorithms and the results have been compared.
Title: Evaluating the Impact of Missing Data Imputation through the use of the Random Forest Algorithm
Abstract: This paper presents an impact assessment for the imputation of missing data. The data set used is HIV Seroprevalence data from an antenatal clinic study survey performed in 2001. Data imputation is performed through five methods: Random Forests, Autoassociative Neural Networks with Genetic Algorithms, Autoassociative Neuro-Fuzzy configurations, and two Random Forest and Neural Network based hybrids. Results indicate that Random Forests are superior in imputing missing data in terms both of accuracy and of computation time, with accuracy increases of up to 32% on average for certain variables when compared with autoassociative networks. While the hybrid systems have significant promise, they are hindered by their Neural Network components. The imputed data is used to test for impact in three ways: through statistical analysis, HIV status classification and through probability prediction with Logistic Regression. Results indicate that these methods are fairly immune to imputed data, and that the impact is not highly significant, with linear correlations of 96% between HIV probability prediction and a set of two imputed variables using the logistic regression analysis.
Title: Pattern Recognition and Memory Mapping using Mirroring Neural Networks
Abstract: In this paper, we present a new kind of learning implementation to recognize the patterns using the concept of Mirroring Neural Network (MNN) which can extract information from distinct sensory input patterns and perform pattern recognition tasks. It is also capable of being used as an advanced associative memory wherein image data is associated with voice inputs in an unsupervised manner. Since the architecture is hierarchical and modular it has the potential of being used to devise learning engines of ever increasing complexity.
Title: Feature Selection By KDDA For SVM-Based MultiView Face Recognition
Abstract: Applications such as face recognition that deal with high-dimensional data need a mapping technique that introduces representation of low-dimensional features with enhanced discriminatory power and a proper classifier, able to classify those complex features. Most of traditional Linear Discriminant Analysis suffer from the disadvantage that their optimality criteria are not directly related to the classification ability of the obtained feature representation. Moreover, their classification accuracy is affected by the "small sample size" problem which is often encountered in FR tasks. In this short paper, we combine nonlinear kernel based mapping of data called KDDA with Support Vector machine classifier to deal with both of the shortcomings in an efficient and cost effective manner. The proposed here method is compared, in terms of classification accuracy, to other commonly used FR methods on UMIST face database. Results indicate that the performance of the proposed method is overall superior to those of traditional FR approaches, such as the Eigenfaces, Fisherfaces, and D-LDA methods and traditional linear classifiers.
Title: Face Detection Using Adaboosted SVM-Based Component Classifier
Abstract: Recently, Adaboost has been widely used to improve the accuracy of any given learning algorithm. In this paper we focus on designing an algorithm to employ combination of Adaboost with Support Vector Machine as weak component classifiers to be used in Face Detection Task. To obtain a set of effective SVM-weaklearner Classifier, this algorithm adaptively adjusts the kernel parameter in SVM instead of using a fixed one. Proposed combination outperforms in generalization in comparison with SVM on imbalanced classification problem. The proposed here method is compared, in terms of classification accuracy, to other commonly used Adaboost methods, such as Decision Trees and Neural Networks, on CMU+MIT face database. Results indicate that the performance of the proposed method is overall superior to previous Adaboost approaches.
Title: Nonparametric Estimation of Variance Function for Functional Data
Abstract: This article investigates nonparametric estimation of variance functions for functional data when the mean function is unknown. We obtain asymptotic results for the kernel estimator based on squared residuals. Similar to the finite dimensional case, our asymptotic result shows the smoothness of the unknown mean function has an effect on the rate of convergence. Our simulaton studies demonstrate that estimator based on residuals performs much better than that based on conditional second moment of the responses.
Title: Standard Logics Are Valuation-Nonmonotonic
Abstract: It has recently been discovered that both quantum and classical propositional logics can be modelled by classes of non-orthomodular and thus non-distributive lattices that properly contain standard orthomodular and Boolean classes, respectively. In this paper we prove that these logics are complete even for those classes of the former lattices from which the standard orthomodular lattices and Boolean algebras are excluded. We also show that neither quantum nor classical computers can be founded on the latter models. It follows that logics are "valuation-nonmonotonic" in the sense that their possible models (corresponding to their possible hardware implementations) and the valuations for them drastically change when we add new conditions to their defining conditions. These valuations can even be completely separated by putting them into disjoint lattice classes by a technique presented in the paper.
Title: Sequential multiple hypothesis testing in presence of control variables
Abstract: Suppose that at any stage of a statistical experiment a control variable $X$ that affects the distribution of the observed data $Y$ at this stage can be used. The distribution of $Y$ depends on some unknown parameter $\theta$, and we consider the problem of testing multiple hypotheses $H_1: \theta=\theta_1$, $H_2: \theta=\theta_2, ...$, $H_k: \theta=\theta_k$ allowing the data to be controlled by $X$, in the following sequential context. The experiment starts with assigning a value $X_1$ to the control variable and observing $Y_1$ as a response. After some analysis, another value $X_2$ for the control variable is chosen, and $Y_2$ as a response is observed, etc. It is supposed that the experiment eventually stops, and at that moment a final decision in favor of one of the hypotheses $H_1,...$, $H_k$ is to be taken. In this article, our aim is to characterize the structure of optimal sequential testing procedures based on data obtained from an experiment of this type in the case when the observations $Y_1, Y_2,..., Y_n$ are independent, given controls $X_1,X_2,..., X_n$, $n=1,2,...$.